Package in.cdac.medinfo.csnotk.csnolib.db

Class QueryManager

java.lang.Object

in.cdac.medinfo.csnotk.csnolib.db.QueryManager

public class QueryManager
extends java.lang.Object

Establishes a connection to fetch data from SNOMED CT database.

Constructor Summary

Constructors

Constructor	Description
QueryManager()

Method Summary

Modifier and Type	Method	Description
void	createcRefsetdb(java.lang.String refsetId, java.lang.String refFilePath, java.util.Set<java.lang.String> moduleIdSet)	This method will create database for cRefset
void	createExtensiondb(java.util.Set<java.lang.String> moduleIdSet, java.lang.String conceptFile, java.lang.String descriptionFile, java.lang.String relationshipFile, java.lang.String refsetLangFile, java.lang.String concreteRelationshipFile, java.lang.String identifierFile)	This method will create SNOMED CT extension database
void	createRefsetdb(java.lang.String refsetId, java.lang.String refFilePath, java.util.Set<java.lang.String> moduleIdSet)	This method will create database for Refset
boolean	createSimpleMapdb(java.lang.String moduleId, java.lang.String simpleMapFilePath)	This method will create database for simpleMap
void	createSNOMEDdb(java.lang.String conceptFile, java.lang.String descriptionFile, java.lang.String relationshipFile, java.lang.String refsetLangFile, java.lang.String textdefinitionFile, java.lang.String concreteRelationshipFile)	This method will create SNOMED CT database
void	deleteRelationshipTempFile(java.lang.String filePath)	This method will delete temporary relationship file created for TC table generation
java.lang.String	exportRelationshipTableAndDeleteTCTable()	This method will export relationship table into a tsv file (for TC table creation)
java.lang.String	getAcceptabilityId(java.lang.String descriptionId)	Returns acceptability Id for specified description id.
java.util.List<Description>	getDescriptions(java.lang.String conceptId)	Returns list of Descriptions associated for a given concept identifier and which is other than FSN.
java.lang.String	getPreferredName(java.lang.String conceptId, EnumLangRefset enumLangRefset)	Returns list of preferred names in US refset associated with corresponding Concept identifier.
java.util.List<Relationship>	getRelationships(java.lang.String ConceptId, java.lang.String relationshipType, EnumDirection direction)	Returns unique Inward/Outward latest relationships with active status.
void	loadClosureTable(java.io.File ct_file)	This function loads the closure table in the database.
void	populateConcept(java.lang.String id, Concept concept)	Returns a SNOMED CT Concept associated for a given concept identifier.
java.util.Set<Concept>	searchConcepts(java.lang.String searchTerm)	Searches for concepts in the SNOMED CT repository for the given search term.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

QueryManager

public QueryManager()

Method Detail

populateConcept

public void populateConcept(java.lang.String id,
                            Concept concept)
                     throws java.sql.SQLException,
                            java.text.ParseException

Returns a SNOMED CT Concept associated for a given concept identifier.

Parameters:

id - identifier of the concept.

concept - SNOMED CT Concept which is to be populated.

Throws:

java.sql.SQLException

java.text.ParseException

getDescriptions

public java.util.List<Description> getDescriptions(java.lang.String conceptId)
                                            throws java.sql.SQLException,
                                                   java.text.ParseException

Returns list of Descriptions associated for a given concept identifier and which is other than FSN.

Parameters:

conceptId - SNOMED CT Concept identifier.

Returns:

List of Descriptions .

Throws:

java.sql.SQLException - if any error occurs while accessing database.

java.text.ParseException

searchConcepts

public java.util.Set<Concept> searchConcepts(java.lang.String searchTerm)
                                      throws java.sql.SQLException

Searches for concepts in the SNOMED CT repository for the given search term.

Parameters:

searchTerm - String term/text to be searched .

Returns:

Set of Concepts.

Throws:

java.sql.SQLException - if any error occurs while accessing database.

getRelationships

public java.util.List<Relationship> getRelationships(java.lang.String ConceptId,
                                                     java.lang.String relationshipType,
                                                     EnumDirection direction)
                                              throws java.sql.SQLException,
                                                     java.text.ParseException

Returns unique Inward/Outward latest relationships with active status.

Parameters:

ConceptId - identifier of the Concept.

enumRelationshipType - specifies the type of relationship.

direction - specifies the direction(source / destination) EnumDirection.

Returns:

Set of Relationships .

Throws:

java.sql.SQLException - if any error occurs while accessing database.

java.text.ParseException

getPreferredName

public java.lang.String getPreferredName(java.lang.String conceptId,
                                         EnumLangRefset enumLangRefset)
                                  throws java.sql.SQLException

Returns list of preferred names in US refset associated with corresponding Concept identifier.

Parameters:

enumLangRefset - specifies the Language Refset EnumLangRefset }.

conceptId - identifier of the Concept.

Returns:

Preferred name of Concept.

Throws:

java.sql.SQLException

loadClosureTable

public void loadClosureTable(java.io.File ct_file)
                      throws java.sql.SQLException,
                             java.io.IOException

This function loads the closure table in the database.

Parameters:

ct_file - File associated with the closure table.

Throws:

java.sql.SQLException

java.io.IOException

getAcceptabilityId

public java.lang.String getAcceptabilityId(java.lang.String descriptionId)
                                    throws java.sql.SQLException

Returns acceptability Id for specified description id. acceptability id indicates whether particular description is Preferred Term or not.

Parameters:

descriptionId - String identifier of the Description.

Returns:

String value that specifies the acceptability id.

Throws:

java.sql.SQLException

createSNOMEDdb

public void createSNOMEDdb(java.lang.String conceptFile,
                           java.lang.String descriptionFile,
                           java.lang.String relationshipFile,
                           java.lang.String refsetLangFile,
                           java.lang.String textdefinitionFile,
                           java.lang.String concreteRelationshipFile)
                    throws java.sql.SQLException

This method will create SNOMED CT database

Parameters:

conceptFile - file path for Concept File

descriptionFile - file path for Description File

relationshipFile - file path for Relationship File

refsetLangFile - file path for Language Refset File

Throws:

java.sql.SQLException

createExtensiondb

public void createExtensiondb(java.util.Set<java.lang.String> moduleIdSet,
                              java.lang.String conceptFile,
                              java.lang.String descriptionFile,
                              java.lang.String relationshipFile,
                              java.lang.String refsetLangFile,
                              java.lang.String concreteRelationshipFile,
                              java.lang.String identifierFile)
                       throws java.sql.SQLException

This method will create SNOMED CT extension database

Parameters:

conceptFile - file path for Concept File

descriptionFile - file path for Description File

relationshipFile - file path for Relationship File

refsetLangFile - file path for Language Refset File

Set - of moduleId

Throws:

java.sql.SQLException

createRefsetdb

public void createRefsetdb(java.lang.String refsetId,
                           java.lang.String refFilePath,
                           java.util.Set<java.lang.String> moduleIdSet)
                    throws java.sql.SQLException

This method will create database for Refset

Parameters:

refsetId -

refFilePath -

Throws:

java.sql.SQLException

createcRefsetdb

public void createcRefsetdb(java.lang.String refsetId,
                            java.lang.String refFilePath,
                            java.util.Set<java.lang.String> moduleIdSet)
                     throws java.sql.SQLException

This method will create database for cRefset

Parameters:

refsetId -

refFilePath -

moduleIdSet -

Throws:

java.sql.SQLException

createSimpleMapdb

public boolean createSimpleMapdb(java.lang.String moduleId,
                                 java.lang.String simpleMapFilePath)
                          throws java.sql.SQLException

This method will create database for simpleMap

Parameters:

moduleId -

simpleMapFilePath -

Throws:

java.sql.SQLException

exportRelationshipTableAndDeleteTCTable

public java.lang.String exportRelationshipTableAndDeleteTCTable()
                                                         throws java.sql.SQLException,
                                                                java.io.IOException

This method will export relationship table into a tsv file (for TC table creation)

Throws:

java.sql.SQLException

java.io.IOException

deleteRelationshipTempFile

public void deleteRelationshipTempFile(java.lang.String filePath)

This method will delete temporary relationship file created for TC table generation